@jscarle, inside the VM there is no hardware NIC, both types are virtual inside a VM in most use cases, not counting the edge case of a passthrough card.
In reality the biggest thing inside the VM in both of the scenarios above is where you are doing the VLAN tagging, either inside VyOS/VIF or via adding multiple NIC to the VM that are tagged and the third way, your NIC(s) in the host is tagged already so your hypervisor switch and any NIC using the switch does not need any VLAN tagging either, ie Windows Server Teaming with Hyper-V.
I guess that these are all the easy part, we appear to all on the same page in terms of the different ways to add interfaces to a VM, the question was more based on the technical differences between different methods of attaching the interfaces, which is much more complex.